TAMPA — When John Franklin took over the Hillsborough County school district’s transportation department in 2007, he was tasked with revamping and reorganizing an operation that was deemed ineffective by consultants, mired as it was in late buses and poor morale.

Seven years later, Franklin is leaving the department as morale problems mount and another review is under way.

Many employees have complained at school board and town hall meetings in recent months about faulty equipment, poor training practices for those who handle medically fragile students and leadership problems.

Many of the complaints have been directed at Franklin, 46, who resigned Tuesday from his $109,599 a year job as transportation general manager.

“I have reiterated to our transportation team that our goal remains unchanged — we work together to safely transport children every day,” schools Superintendent MaryEllen Elia said in a news release Wednesday morning.

Once again, a consultant is conducting a review of the department, with the ultimate goal of updating the district’s aging school bus fleet. His review, along with feedback gathered from employees, will be compiled into an action plan to be presented to the school board in early May.

School board member April Griffin said she wasn’t surprised to hear about Franklin’s departure.

“He had a daunting task,” she said. “All of these issues – the successes and the failures alike – do not fully rest on his shoulders.”

Elia also sent an automated message to employees, saying, “Unfortunately, there are forces at play inside and outside of our district that are intent on causing dissension and pressure in making our jobs more difficult. That has led to good people to choose to leave our district to pursue other opportunities.”

Board member Candy Olson took issue with the message.

“I wish she hadn’t said it,” Olson said. “It makes it more emotional when the boss says that.”

Before taking the job in Hillsborough, Franklin was a schools transportation director in San Antonio, Texas. In Hillsborough, he received high marks on his annual evaluations

Chris Farkas, the district’s new chief facilities officer, will oversee the department as a nationwide search is conducted for Franklin’s replacement.

Franklin could not be reached for comment Wednesday. He wrote in a resignation letter to Farkas Tuesday night that the best thing for him to do now is explore other opportunities.

“I would like to reserve my greatest appreciation for the hundreds of hard-working and dedicated transportation department employees who faithfully serve students each day in many different capacities,” he wrote.

Olson said Franklin’s resignation is a “huge loss.”

“The kind of attacks that have been leveled at him can only go so far,” she said. “It’s also an opportunity. This gives us a chance to think about what skill sets we need in transportation.”

The eighth-largest school district in the nation, Hillsborough will spend $66 million of its nearly $3 billion budget on transportation this year. The department is responsible for transporting 90,000 students to and from school every day, and is staffed with more than 1,200 employees.

Griffin believes the transportation department should be converted into a district division and that the general manager position should be changed to an assistant superintendent job. Whoever fills it would report directly to Elia.

“I want someone with a vast knowledge of what the job entails, along with the personality to bring this department back together,” Griffin said.